Universal behavior of localization of residue fluctuations in globular proteins

Localization properties of residue fluctuations in globular proteins are studied theoretically by using the Gaussian network model. Participation ratio for each residue fluctuation mode is calculated. It is found that the relationship between participation ratio and frequency is similar for all globular proteins, indicating a universal behavior in spite of their different size, shape, and architecture.Comment: 4 pages, 3 figures. To appear in Phys. Rev.

Immunoprotective role of indoleamine 2,3-dioxygenase in engraftment of allogenic skin substitute in wound healing

Delayed wound healing can significantly impact survival of patients who suffer from severe thermal injury. In general, the use of a wound coverage, particularly with those of bilayer skin substitute, would be ideal to promote healing and prevent infection and fluid loss. Although the use of an autologous skin substitute is desirable, its preparation is time consuming and its immediate availability is impossible. To overcome this difficulty, the authors have previously demonstrated that the expression of indoleamine 2,3 dioxygenase (IDO) could function as a local immune suppressive factor in protecting allogenic fibroblasts and keratinocytes without using any immunosuppressive medication in a wound healing animal model. IDO, which is naturally expressed in the placenta by trophoblast cells during pregnancy, plays an essential role in maternal tolerance toward the fetus. The potent and selective local immunosuppressive function of IDO makes this enzyme a very promising tool for engineering a nonrejectable skin allograft. Here, the authors reviewed and discussed how the expression of IDO by the primary cells of our skin substitute can serve as a source of IDO enzyme activity and generate a tryptophan-deficient environment. Under this condition, only skin cells but not immune cells (CD4+ and CD8+ cells) would survive and protect engraftment of this engineered and shelf-ready skin substitute to be used not only as wound coverage but also as a rich source of wound healing promoting factors. Therefore, this review summarizes the body of work on immunoprotective role of IDO in engraftment of allogenic skin substitute in wound healing, which has recently been reported by the authors' research group and others. Copyright © 2012 by the American Burn Association

Molecular characterization of polymorphisms among Pseudomonas aeruginosa strains isolated from burn patients' wounds

Pseudomonas aeruginosa is one of the most common reasons for nosocomial infections. Given the high morbidity and mortality, as well as the cost of management, particularly in developing countries, burn injuries are considered important health concerns. Owing to the increased rate of resistance against antibiotics, this study aimed to isolate Pseudomonas aeruginosa strains from burn patient's wounds by analyzing antibiotic susceptibility and genetic profiling. In this regard, we explored the relationship between the nucleotide sequence and antibiotic susceptibility. In this cross-sectional study, 107 isolates of P. aeruginosa were collected from a major burn center in Tehran, Iran. The isolates were characterized with standard biochemical tests and examined by applying the Disk Diffusion method to find the patterns of sensitivity, and their genetic relationship was revealed by RAPD-PCR method. According to the antibiogram results, most of the isolates were resistant to 3 or more antibiotics tested and the most sensitivity was related to the Colistin antibiotic. RAPD-PCR method revealed a high polymorphism among P. aeruginosa isolates in Tehran. There was no significant association between the genotype groups and antibiotic susceptibility profiles. We evaluated the pattern of resistance to pathogenic organisms and identified multi-drug resistant organisms. Currently, Colistin antibiotic is the most suitable treatment option for burned patients. RAPD-PCR is a genotyping method with high efficiency for typing and categorizing different isolates of MDR-P. aeruginosa. © 2020 Biotechnology; Genetics; Microbiology; Molecular Biology; Infectious disease; Pseudomonas aeruginosa; RAPD-PCR; Nosocomial infections; Burn patients. © 202

Point Mutations on Mitochondrial DNA in Iranian Patients with Friedreich’s Ataxia

ObjectiveMitochondrial DNA (mtDNA) is considered a candidate modifier factor for neuro-degenerative disorders. The most common type of ataxia is Friedreich's ataxia (FA). The aim of this study was to investigate different parts of mtDNA in 20 Iranian FA patients and 80 age-matched controls by polymerase chain reaction (PCR) and automated DNA sequencing methods to find any probable point mutations involved in the pathogenesis of FA.Materials and MethodsWe identified 13 nucleotide substitutions including A3505G, T3335C, G3421A, G8251A, A8563G, A8563G, G8584A, T8614C, T8598C, C8684T, A8701G, G8994A and A9024G.ResultsTwelve of 13 nucleotide substitutions had already been reported as polymorphism. One of the nucleotide substitutions (A9024G) had not been reported before. The A9024G nucleotide substitution does not change its amino acid. The controls were also investigated for this polymorphism which was found in two of them (2.5%).ConclusionNone of the mutations found in this study can affect the clinical manifestations of FA. This survey also provides evidence that the mtDNA A9024G allele is a new nonpathogenic polymorphism. We suggest follow-up studies for this polymorphism in different populations.

Genetic diversity of the common bacterial blight pathogen of bean, Xanthomonas axonopodis pv. phaseoli, in Iran revealed by rep-PCR and PCR–RFLP analyses

Xanthomonad-like bacteria that are associated with common bacterial blight of bean in Iran were identified on the basis of their colonial morphology, biochemical and serological properties, presence of a specific DNA fragment using PCR primers and pathogenicity on bean. Xanthomonas axonopodis pv. phaseoli (Xap) strains were further characterized using rep-PCR and restriction fragment length polymorphism (RFLP). RFLP profiles generated by the restriction endonucleases RsaI, TaqI, HaeIII and Sau96I and rep-PCR analysis revealed that Iranian strains were relatively genetically homogenous. The similarity coefficients among the strains ranged from 0.87 to 1. The genetic diversity coefficients among strains from three infected provinces, Isfahan, Markazi and Lorestan, were 0.019, 0.072 and 0.033, respectively. The low overall level of polymorphism within Xap isolates collected from the three Iranian infected regions could suggest that few initial inoculum introductions might have distributed among these different bean-growing areas in Iran

Investigation on mitochondrial tRNALeu/Lys, NDI and ATPase 6/8 in Iranian multiple sclerosis patients

As with chromosomal DNA, the mitochondrial DNA (mtDNA) can contain mutations that are highly pathogenic .In fact, many diseases of the central nervous system are known to be caused by mutations in mtDNA. Dysfunction of the mitochondrial Respiratory Chain (RC) has been shown in patients with neurological disease including Alzheimer's disease (AD), Parkinson's disease (PD) and Multiple sclerosis (MS). MS is a demyelinating disease of central nervous system characterized by morphological hallmarks of inflammation, demyelination and axonal loss. Considering this importance, we decided to investigate several highly mutative parts of mtDNA for point mutations as MT-LTI (tRNALeucine1(UUA/G)), MT-NDI (NADH Dehydrogenase subunit 1), MT-COII (Cytochrome c oxidase subunit II), MT-TK (tRNALysine), MT-ATP8 (ATP synthase subunit F0 8) and MT-ATP6 (ATP synthase subunit F0 6) in 20 Iranian MS patients and 80 age-matched control subjects by PCR and automated DNA sequencing to evaluate any probable point mutations. Our results revealed that 15 (75) out of 20 MS patients had point mutations. Some of point mutations were newly found in this study. This study suggested that point mutation occurred in mtDNA might be involved in pathogenesis of MS. © 2007 Springer Science+Business Media, LLC

Serum IL-33 Is Elevated in Children with Asthma and Is Associated with Disease Severity

Background: The role of IL-33, a member of the IL-1 family, in airway hyperresponsiveness and asthma has still to be fully understood. Objectives: This study is aimed at investigating serum IL-33 in children with asthma and its association with asthma severity. Methods: This age- and sex-matched case-control study comprised 61 children with asthma and 63 healthy controls. The mean age of the participants was 9.21 years (range: 6-14). Serum IL-33 was measured using ELISA and was compared between children with asthma and controls. In addition, the association of serum IL-33 with asthma severity was investigated. Results: The level of serum IL-33 was significantly higher in children with asthma than in controls (15.17 ± 32.3 vs. 0.61 ± 2.16 pg/ml; p = 0.028). It was significantly increased proportionately to asthma severity, namely 9.92 ± 30.26 pg/ml in children with mild asthma, 13.68 ± 29.27 pg/ml in children with moderate asthma and 31.92 ± 41.45 pg/ml in children with severe asthma (p = 0.026). Conclusion: Serum IL-33 is increased in children with asthma and is associated with disease severity. © 2016 S. Karger AG, Basel

FTO genotype and weight loss: systematic review and meta-analysis of 9563 individual participant data from eight randomised controlled trials

Objective To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. Design Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. Data sources Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. Eligibility criteria for study selection Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after dietary, physical activity, or drug based interventions. Gene by treatment interaction models were fitted to individual participant data from all studies included in this review, using allele dose coding for genetic effects and a common set of covariates. Study level interactions were combined using random effect models. Metaregression and subgroup analysis were used to assess sources of study heterogeneity. Results We identified eight eligible randomised controlled trials for the systematic review and meta-analysis (n=9563). Overall, differential changes in body mass index, body weight, and waist circumference in response to weight loss intervention were not significantly different between FTO genotypes. Sensitivity analyses indicated that differential changes in body mass index, body weight, and waist circumference by FTO genotype did not differ by intervention type, intervention length, ethnicity, sample size, sex, and baseline body mass index and age category. Conclusions We have observed that carriage of the FTO minor allele was not associated with differential change in adiposity after weight loss interventions. These findings show that individuals carrying the minor allele respond equally well to dietary, physical activity, or drug based weight loss interventions and thus genetic predisposition to obesity associated with the FTO minor allele can be at least partly counteracted through such interventions. Systematic review registration PROSPERO CRD42015015969

PRODUKTIVITAS TENAGA PENGARIT BERDASARKAN MODA PENGANGKUT DI PETERNAKAN SAPI PERAH PONDOK RANGGON, JAKARTA TIMUR

Penelitian ini bertujuan untuk menganalisis produktivitas tenaga pengarit dan efektivitasnya berdasarkan moda pengangkut yang dipergunakan di peternakan sapi perah Pondok Ranggon, Jakarta Timur. Peternakan sapi perah Pondok Rangon merupakan salah satu peternakan yang masih bertahan di DKI Jakarta yang ketersediaan hijauan pakannya berasal pada padang rumput alam. Penelitian didasarkan pada sumber data primer dan sekunder dengan cara sensus dari total 22 peternak. Hasil penelitian menunjukkan bahwa karakteristik peternak di Pondok Rangon 40,91% telah berumur > 55 tahun dan 45,46% telah memiliki pengalaman >20 tahun. Kapasitas mengarit tertinggi pada umur 38 tahun (395 kg/hari) dan moda truck lebih efisien dalam penyediaan hijauan dibanding pick up dan becak motor

Imipenem-resistant Pseudomonas aeruginosa strains carry metallo-β-lactamase gene blaVIM in a level i Iranian burn hospital

Introduction: In this study, we aimed to determine the distribution of blaVIM and blaIMP transferable genes in Pseudomonas aeruginosa isolates from infected burn wounds in an Iranian level I burn care center. These genes confer imipenem resistance and increase the mortality rate of burn patients. Methods: P. aeruginosa isolates from burn patients were tested for antibiotic susceptibility with Kirby-Bauer disk diffusion method and for production of metallo-β-lactamase (MBL) by EDTA disk method. DNA was purified from isolates with positive MBL results and underwent PCR for detection of blaVIM and blaIMP genes. Results: MBL was produced by 23 imipenem-resistant isolates and blaVIM gene was detected in all of these isolates. None of the isolates carried blaIMP gene. Mortality rate of infection with MBL-producing Pseudomonas strains was 82.6 in this hospital while the mortality rate for non-MBL-producing Pseudomonas was 22.7. Conclusion: We found that all MBL-producing isolates in this hospital carry blaVIM gene. This result is similar to the previous Iranian study and emphasizes the importance of VIM family of MBLs in Iran. Timely identification of these strains and strict isolation methods can prevent spread of this transferable gene to other Gram-negative bacteria and prevent the subsequent outbreak of high mortality. © 2009 Elsevier Ltd and ISBI